| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2023-07-21 | Rename 'gn-id' prefix to 'gn' | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-07-21 | Replace :gn with :gn-id and :gn-term | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-07-21 | Dump phenotypes with documentation. | Munyoki Kilyungi | |
| 2023-07-21 | Make the default ontology "gn-id:" | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-07-21 | Dump probeset metadata with documentation | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-07-21 | Update tissue dump to use gn-term/gn-id | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-07-21 | Replace gn with gn-term and gn-id where suitable | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-07-21 | Use size of the results set to come up with sparql example | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-07-21 | Replace gn:species with gn-species | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-07-21 | Update dump-species to have lists for inputs and output | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-07-21 | Add "gn:species:" prefix | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-07-21 | Convert symbol to a string when show-casing triples in doc | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-07-21 | Capitalize species identifier | Munyoki Kilyungi | |
| Replace gn:species_mus_musculus with gn:species:Mus_musculus. | |||
| 2023-07-21 | Add string-capitalize-first | Munyoki Kilyungi | |
| * dump/strings.scm: Export string-capitalize-first (string-capitalize-first): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-07-21 | Make string->identifier take optional keyword args | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-07-21 | Make dump-data? default to #f when dumping data | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-07-21 | Rewrite dump-with-documentation to be order-agnostic | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-07-21 | Dump dataset metadata with documentation | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-07-21 | Dump publication metadata with documentation | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-07-21 | Dump tissue metadata with documentation | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-07-21 | Dump species metadata with documentation | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-07-21 | Conditionally dump documentation | Munyoki Kilyungi | |
| 2023-07-21 | Make prefix function have an optional ttl? | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-07-21 | Revert "Pass port as an optional argument" | Munyoki Kilyungi | |
| This reverts commit 195ca590be5533935cf708d49fcb3736b3c78643. | |||
| 2023-07-21 | Add missing srfi-26 import | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-07-21 | Create a new procedure for shadowing a file port | Munyoki Kilyungi | |
| * dump/documentation.scm (dump): Export call-with-documentation. (call-with-documentation): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-07-21 | Rename auto-documentation-port -> path | Munyoki Kilyungi | |
| We don't need to pass around ports as part of a configuration when we can instead pass in a path that can be used to open a port. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-07-21 | Move dump-configuration record type to (dump documentation) | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-07-21 | Construct example SQL query and expected results | Munyoki Kilyungi | |
| 2023-07-21 | Pass port to scm->triples | Munyoki Kilyungi | |
| * dump/triples.scm (scm->triples): Make define have an optional arg fn that defaults to "triple". | |||
| 2023-07-21 | Pass port as an optional argument | Munyoki Kilyungi | |
| * dump/triples.scm (triple): Add port as an optional argument. Defaults to #t. This enables us to use triple to print to other ports E.g in the case of dumping documentation to a different file. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-07-21 | Print out triples with the from Table.Name or Table.Alias | Munyoki Kilyungi | |
| * dump/special-forms.scm (field->datum): New function. (define-dump): Use the field->datum to convert triples into the form Table.Name or Table.Alias. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-07-21 | Add table metadata to triple dump | Munyoki Kilyungi | |
| 2023-07-21 | Add a section sub-heading for schema triples | Munyoki Kilyungi | |
| 2023-07-21 | Wrap the dump title in quotes | Munyoki Kilyungi | |
| 2023-07-21 | Replace #` with #'when fetching the name of the defined dump | Munyoki Kilyungi | |
| 2023-07-21 | Use call-with-target-database when dumping schema annotations | Munyoki Kilyungi | |
| * dump/schema-dump.scm (dump-schema-annotations): Replace call-with-genenetwork-database with call-with-target-database. | |||
| 2023-07-21 | Conditionally autogenerate schema triples during dump | Munyoki Kilyungi | |
| 2023-07-21 | Rename dump-configuration slots | Munyoki Kilyungi | |
| * dump/special-forms.scm: Export dump-configuration? Rename dump-configuration-table-metadata -> dump-configuration-triples?; dump-configuration-table-dump -> dump-configuration-table-metadata?; and dump-configuration-auto-document-path -> dump-configuration-auto-documentation-port (<dump-configuration>): Ditto renames. (dump-configuration): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-07-21 | Make dumping optional, defaulting to #t | Munyoki Kilyungi | |
| There may be a case where one just wants to dump metadata about the s-exps only. | |||
| 2023-07-21 | Add table-dump? option to dump-configuration record | Munyoki Kilyungi | |
| * dump/special-forms.scm: Export dump-configuration-table-dump?. (<dump-configuration>): Add dump-configuration-table-dump. (dump-configuration): Make table-dump? default to #t. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-07-21 | Optionally self-document while dumping | Munyoki Kilyungi | |
| 2023-07-21 | Add a configuration record-type for for the define macro | Munyoki Kilyungi | |
| * dump/special-forms.scm: Import (srfi srfi-9 gnu). (<dump-configuration>): New record-type. (define-dump): Use the above record-type. | |||
| 2023-07-18 | Ignore emacs temporary backup files | Frederick Muriuki Muriithi | |
| 2023-06-28 | Updated species.ttl | Pjotr Prins | |
| 2023-06-28 | Add species mapping to wikidata to schema | Pjotr Prins | |
| 2023-06-26 | Add "-m manifest.scm" flag to guix shell commands | Munyoki Kilyungi | |
| 2023-06-24 | Fix documentation errors that were leading to confusion | Frederick Muriuki Muriithi | |
| 2023-06-24 | Add some missing dependencies | Frederick Muriuki Muriithi | |
| 2023-06-21 | Fix failing tests | Munyoki Kilyungi | |
| * dump/special-forms.scm: Export map-alist. * tests.scm: Import strings, and special-forms. | |||
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index : gn-transform-databases | |
| Data transformers for GeneNetwork (particularly to RDF) |
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